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Nucleic Acids Research Advance Access originally published online on January 26, 2007
Nucleic Acids Research 2007 35(4):e27; doi:10.1093/nar/gkl1120
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Nucleic Acids Research, 2007, Vol. 35, No. 4 e27
© 2007 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Specific residues at every third position of siRNA shape its efficient RNAi activity

Takayuki Katoh and Tsutomu Suzuki*

Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan

*To whom correspondence should be addressed. Tel: +81 3 5841 8752; Fax: +81 3 3816 0106; Email: ts{at}chembio.t.u-tokyo.ac.jp

Received September 4, 2006. Revised October 3, 2006. Accepted December 7, 2006.

Small interfering RNA (siRNA) induces sequence-specific post-transcriptional gene silencing in mammalian cells. Different efficacy of each siRNA is considered to result from sequence preference by protein components in RNAi. To obtain mechanistic insight into siRNA functionality, here we describe a complete data set of siRNA activities targeting all possible position of a single mRNA in human cells. Seven hundred and two siRNAs covering open reading frame of enhanced green fluorescent protein mRNA ( 720 bases) were examined with minimized error factors. The most important finding is that specific residues at every third position of siRNAs greatly influence its RNAi activity; the optimized base composition at positions 3n + 1 (4,7,10,13,16,19) in siRNAs have positive effects on the activity, which can explain the waving siRNA activity with 3 nucleotides (nt) periodicity in the sequential positions of mRNAs. Since there was an obvious correlation between siRNA activity and its binding affinity to TRBP, a partner protein of human Dicer, the 3-nt periodicity might correlate with the affinity to TRBP. As an algorithm (‘siExplorer’) developed by this observation successfully calculated the activities of siRNAs targeting endogenous human genes, the 3-nt periodicity provides a new aspect unveiling siRNA functionality.

The nomenclature for mixed bases used in this study obey the rules previously established in the literature (59), namely, R is A or G, Y is U or C, W is A or U, S is G or C, and N is all bases (A, U, G or C). The algorithm for predicting siRNA activity is available as ‘siExplorer’ (http://rna.chem.t.u-tokyo.ac.jp/siexplorer.htm).


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[Abstract] [Full Text] [PDF]


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